LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem       ###
### using energy-conserving DPD (eDPD) simulation                    ###
###                                                                  ###
### Created  : Zhen Li (zhen_li@brown.edu)                           ###
###            Division of Applied Mathematics, Brown University.    ###
###                                                                  ###
### mDPD system setup follows Fig.12 in the publication:             ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis.      ###
### "Energy-conserving dissipative particle dynamics with            ###
### temperature-dependent properties". J. Comput. Phys.,             ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003               ###
########################################################################
units                   lj
dimension               3
boundary                p p p
neighbor                0.2 bin
neigh_modify        every 1 delay 0 check yes

atom_style              edpd
comm_modify vel yes

region     edpd     block -10 10 -10 10 -5 5 units box
create_box          1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
  1 by 1 by 1 MPI processor grid
create_atoms        1 random 16000 276438 NULL
Created 16000 atoms
  using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
  create_atoms CPU = 0.002 seconds
mass                1 1.0
set                 atom * edpd/temp 1.0
Setting atom values ...
  16000 settings made for edpd/temp
set                 atom * edpd/cv 1.0E5
Setting atom values ...
  16000 settings made for edpd/cv

pair_style          edpd 1.58 9872598
#pair_coeff          1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff          1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58                         power 10.54 -3.66 3.44 -4.10                         kappa -0.44 -3.21 5.04  0.00

compute             mythermo all temp
thermo              100
thermo_modify       temp mythermo
thermo_modify       flush yes

velocity            all create 1.0 432982 loop local dist gaussian

fix         mvv     all mvv/edpd 0.5
fix         upper   all edpd/source cuboid 0.0  5.0 0.0 20.0 10.0 10.0  0.01
fix         lower   all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01

timestep            0.01
run                 500

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair edpd command: doi:10.1016/j.jcp.2014.02.003

@Article{ZLi2014_JCP,
 author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G. E.},
 title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties},
 journal = {Journal of Computational Physics},
 year =    {2014},
 volume =  {265},
 pages =   {113--127}
}

@Article{ZLi2015_CC,
 author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G. E.},
 title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers},
 journal = {Chemical Communications},
 year =    {2015},
 volume =  {51},
 pages =   {11038--11040}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.78
  ghost atom cutoff = 1.78
  binsize = 0.89, bins = 23 23 12
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair edpd, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   1              48.942039      0              50.441946      201.43068    
       100   0.99644296     43.749732      0              45.244303      200.44316    
       200   0.98985852     43.699081      0              45.183776      197.29314    
       300   1.0062075      43.708406      0              45.217622      194.61595    
       400   0.99858259     43.69758       0              45.19536       196.87253    
       500   0.99991379     43.677571      0              45.177348      194.59785    
Loop time of 48.2916 on 1 procs for 500 steps with 16000 atoms

Performance: 8945.662 tau/day, 10.354 timesteps/s, 165.660 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 43.121     | 43.121     | 43.121     |   0.0 | 89.29
Neigh   | 4.5712     | 4.5712     | 4.5712     |   0.0 |  9.47
Comm    | 0.28793    | 0.28793    | 0.28793    |   0.0 |  0.60
Output  | 0.00040031 | 0.00040031 | 0.00040031 |   0.0 |  0.00
Modify  | 0.24651    | 0.24651    | 0.24651    |   0.0 |  0.51
Other   |            | 0.06435    |            |       |  0.13

Nlocal:          16000 ave       16000 max       16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          14106 ave       14106 max       14106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         749963 ave      749963 max      749963 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 749963
Ave neighs/atom = 46.872687
Neighbor list builds = 181
Dangerous builds = 0
reset_timestep      0

compute     temp    all edpd/temp/atom
compute     ccT     all chunk/atom bin/1d y 0.0 1.0
fix         stat    all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile

run                 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.6 | 12.6 | 12.6 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0.99991379     43.67752       0              45.177297      195.4932     
       100   1.0053402      43.685038      0              45.192954      196.73683    
       200   1.0052797      43.665955      0              45.173781      198.60396    
       300   0.98694632     43.650877      0              45.131204      199.11464    
       400   1.003189       43.639966      0              45.144655      196.20663    
       500   1.008172       43.625425      0              45.137589      196.69792    
Loop time of 47.2499 on 1 procs for 500 steps with 16000 atoms

Performance: 9142.877 tau/day, 10.582 timesteps/s, 169.313 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 42.09      | 42.09      | 42.09      |   0.0 | 89.08
Neigh   | 4.4695     | 4.4695     | 4.4695     |   0.0 |  9.46
Comm    | 0.28364    | 0.28364    | 0.28364    |   0.0 |  0.60
Output  | 0.00041768 | 0.00041768 | 0.00041768 |   0.0 |  0.00
Modify  | 0.34551    | 0.34551    | 0.34551    |   0.0 |  0.73
Other   |            | 0.06079    |            |       |  0.13

Nlocal:          16000 ave       16000 max       16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          14131 ave       14131 max       14131 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         749932 ave      749932 max      749932 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 749932
Ave neighs/atom = 46.87075
Neighbor list builds = 182
Dangerous builds = 0
Total wall time: 0:01:35
